<p>In the container yard, the two cranes work in cooperation through handshake bays. The handshake bay, coupled with multiple operations decisions, poses significant challenges for scheduling. To ensure the efficiency of shoreside operations, a significant portion of loading must be prioritized during specific periods under the rule known as “loading-first”. However, this operational rule frequently requires task priorities to be adjusted, and the crane operation schedule must be continuously updated to meet on-site operational requirements. To optimize the selection of handshake bays under the loading-first rule, this paper addresses the synchronized scheduling problem for twin crane performing handover operations. Three Mixed-linear integer programming models with complex and practical coupling constraints are proposed to minimize the makespan. Additionally, a re-optimization approach based on batch task assignment is designed to address the complexity and enhance synchronization. To solve the large problem, a genetic algorithm with variable neighborhood search is developed. The proposed algorithm focuses on both elite-preserving and inferior-accepting search strategies, which help enhance search diversity and prevent the solution from converging to local optimal. Numerical experiments reveal that the variable handshake bay shortens the makespan of loading and unloading operations by an average of 10.52% compared with the fixed one. In loading-first rule, some tasks need to be re-optimized to reduce the coupling degree between two cranes, thereby increasing the makespan. Thus, the proposed synchronized scheduling can reduce crane potential conflicts. This study provides an innovative modelling and computational approach for practice-originated operational optimization, which is expected to explore an effective technique for synchronized scheduling.</p>